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Setd2 SET domain containing 2 [ Mus musculus (house mouse) ]

Gene ID: 235626, updated on 24-Jan-2023

Summary

Official Symbol
Setd2provided by MGI
Official Full Name
SET domain containing 2provided by MGI
Primary source
MGI:MGI:1918177
See related
Ensembl:ENSMUSG00000044791 AllianceGenome:MGI:1918177
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
KMT3A; 4921524K10Rik
Summary
Enables histone methyltransferase activity (H3-K36 specific). Involved in endodermal cell differentiation; histone H3-K36 trimethylation; and stem cell differentiation. Acts upstream of or within several processes, including animal organ development; peptidyl-lysine methylation; and tube morphogenesis. Located in chromosome and nucleus. Is expressed in 1-cell stage embryo; 2-cell stage embryo; 4-cell stage embryo; 8-cell stage embryo; and inner cell mass. Human ortholog(s) of this gene implicated in carcinoma (multiple); gastrointestinal system cancer (multiple); idiopathic pulmonary fibrosis; and malignant mesothelioma. Orthologous to human SETD2 (SET domain containing 2, histone lysine methyltransferase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 11.9), CNS E14 (RPKM 11.1) and 28 other tissues See more
Orthologs
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Genomic context

See Setd2 in Genome Data Viewer
Location:
9; 9 F2
Exon count:
25
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (110361368..110447701)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (110532500..110618633)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene kelch-like 18 Neighboring gene kinesin family member 9 Neighboring gene neurotrophin receptor associated death domain Neighboring gene neurobeachin-like 2 Neighboring gene microRNA 8107

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables alpha-tubulin binding ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K36 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3K36 methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K36 methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K36 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone lysine N-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein-lysine N-methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA repair IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell migration involved in vasculogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cellular response to DNA damage stimulus IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within coronary vasculature morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in defense response to virus ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within embryonic organ development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within embryonic placenta morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in endodermal cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within forebrain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in histone H3-K36 dimethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H3-K36 methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in histone H3-K36 trimethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in histone H3-K36 trimethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone lysine methylation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within immune system process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within innate immune response IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within mesoderm morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in microtubule cytoskeleton organization involved in mitosis ISO
Inferred from Sequence Orthology
more info
 
involved_in mismatch repair ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within morphogenesis of a branching structure IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within neural tube closure IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nucleosome organization ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within peptidyl-lysine trimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in peptidyl-lysine trimethylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within pericardium development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of interferon-alpha production ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of ossification ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of cytokinesis ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of mRNA export from nucleus ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of protein localization to chromatin ISO
Inferred from Sequence Orthology
more info
 
involved_in response to type I interferon ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within stem cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in stem cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in transcription elongation by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within vasculogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in chromosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in chromosome IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETD2
Names
SET domain-containing protein 2
lysine N-methyltransferase 3A
protein-lysine N-methyltransferase SETD2
NP_001074809.2
XP_006512151.1
XP_006512154.1
XP_006512155.1
XP_036010808.1
XP_036010809.1
XP_036010810.1
XP_036010811.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001081340.3NP_001074809.2  histone-lysine N-methyltransferase SETD2

    See identical proteins and their annotated locations for NP_001074809.2

    Status: VALIDATED

    Source sequence(s)
    AC132103
    Consensus CDS
    CCDS40781.2
    UniProtKB/Swiss-Prot
    E9Q5F9, Q8K0F3
    Related
    ENSMUSP00000116313.3, ENSMUST00000153838.8
    Conserved Domains (6) summary
    pfam05279
    Location:19142096
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14691523
    AWS; associated with SET domains
    smart00317
    Location:15241647
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16481664
    PostSET; Cysteine-rich motif following a subset of SET domains
    pfam00397
    Location:23642393
    WW; WW domain
    pfam08236
    Location:24422521
    SRI; SRI (Set2 Rpb1 interacting) domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000075.7 Reference GRCm39 C57BL/6J

    Range
    110361368..110447701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036154915.1XP_036010808.1  histone-lysine N-methyltransferase SETD2 isoform X1

  2. XM_036154916.1XP_036010809.1  histone-lysine N-methyltransferase SETD2 isoform X3

    Conserved Domains (4) summary
    smart00570
    Location:14831537
    AWS; associated with SET domains
    cd19172
    Location:15371678
    SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins
    pfam00397
    Location:23772406
    WW; WW domain
    pfam08236
    Location:24532541
    SRI; SRI (Set2 Rpb1 interacting) domain
  3. XM_036154917.1XP_036010810.1  histone-lysine N-methyltransferase SETD2 isoform X4

    Conserved Domains (4) summary
    smart00570
    Location:14781532
    AWS; associated with SET domains
    cd19172
    Location:15321673
    SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins
    pfam00397
    Location:23732402
    WW; WW domain
    pfam08236
    Location:24492537
    SRI; SRI (Set2 Rpb1 interacting) domain
  4. XM_006512088.5XP_006512151.1  histone-lysine N-methyltransferase SETD2 isoform X2

    Conserved Domains (5) summary
    pfam05279
    Location:19272109
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14821536
    AWS; associated with SET domains
    pfam00397
    Location:23772406
    WW; WW domain
    pfam08236
    Location:24552542
    SRI; SRI (Set2 Rpb1 interacting) domain
    cd19172
    Location:15361677
    SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins
  5. XM_006512091.5XP_006512154.1  histone-lysine N-methyltransferase SETD2 isoform X5

    Conserved Domains (5) summary
    pfam05279
    Location:19222104
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14771531
    AWS; associated with SET domains
    pfam00397
    Location:23722401
    WW; WW domain
    pfam08236
    Location:24502537
    SRI; SRI (Set2 Rpb1 interacting) domain
    cd19172
    Location:15311672
    SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins
  6. XM_006512092.5XP_006512155.1  histone-lysine N-methyltransferase SETD2 isoform X6

    Conserved Domains (5) summary
    pfam05279
    Location:19192101
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14741528
    AWS; associated with SET domains
    pfam00397
    Location:23692398
    WW; WW domain
    pfam08236
    Location:24472534
    SRI; SRI (Set2 Rpb1 interacting) domain
    cd19172
    Location:15281669
    SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins
  7. XM_036154918.1XP_036010811.1  histone-lysine N-methyltransferase SETD2 isoform X7

RNA

  1. XR_004935430.1 RNA Sequence

    Related
    ENSMUST00000196814.5
  2. XR_004935431.1 RNA Sequence

  3. XR_004935429.1 RNA Sequence